Changes

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Merges duplicate variants by position with the option of considering alleles.  (This just discards the duplicate variant that appears later in the VCF file)

Discovers variants from reads in a BAM file.

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   #merge duplicate variants and save output in mills.merged.vcf

   #discover variants from NA12878.bam and write to stdout

   vt discover -b NA12878.bam -s NA12878 -r hs37d5.fa -i 20 -v snps,indels,mnps

   vt discover -b NA12878.bam -s NA12878 -r ~/ref/genome/hs37d5.fa -i 20 -v snps,indels,mnps

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usage : vt discover [options]  

usage : vt discover [options]